changing command name classify.shared to classifyrf.shared

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 6397e358de806f08695d0707c6539352a282be44..f36f1ba23a6af6c9110dc0aac103054ceefedaff 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> GetRelAbundCommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "",false,false); parameters.push_back(pscale);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","relabund",false,true, true); parameters.push_back(pshared);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "","",false,false); parameters.push_back(pscale);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -40,7 +40,7 @@ string GetRelAbundCommand::getHelpString(){
                helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";
                helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
                helpString += "The get.relabund command outputs a .relabund file.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -49,6 +49,21 @@ string GetRelAbundCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string GetRelAbundCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "relabund")      {   pattern = "[filename],relabund";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetRelAbundCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(){      
        try {
                abort = true; calledHelp = true; 
@@ -69,6 +84,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -110,7 +126,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -130,7 +146,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                        else { 
                                pickedGroups = true;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "totalgroup"; }
@@ -153,7 +169,9 @@ int GetRelAbundCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+               string outputFileName = getOutputFileName("relabund", variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -169,11 +187,12 @@ int GetRelAbundCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                getRelAbundance(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -186,7 +205,7 @@ int GetRelAbundCommand::execute(){
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
                                lookup = input->getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                               
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                getRelAbundance(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -200,13 +219,13 @@ int GetRelAbundCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  outputTypes.clear();  m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str());  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -227,18 +246,18 @@ int GetRelAbundCommand::execute(){
                        lookup = input->getSharedRAbundVectors(lastLabel);
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                       
+                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                        getRelAbundance(lookup, out);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                }
        
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                delete input; 
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();